Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
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Acknowledgements This work has been supported from the following funding sources: German Ministry of Education and Research (BMBF) grant 0314000 ‘‘BARLEX’’ to K.F.X.M., M.P., U.S. and N.S.; Leibniz Association grant (Pakt f. Forschung und Innovation) to N.S.; European project of the 7th framework programme ‘‘TriticeaeGenome’’ to R.W., A.S., K.F.X.M., M.M. and N.S.; SFB F3705, of the Austrian Wissenschaftsfond (FWF) to K.F.X.M.; ERA-NET PG project ‘‘BARCODE’’ grant to M.M., N.S. and R.W.; Scottish Government/BBSRC grant BB/100663X/1 to R.W., D.M., P.H., J.R., M.C. and P.K.; National Science Foundation grant DBI 0321756 ‘‘Coupling EST and Bacterial Artificial Chromosome Resources to Access the Barley Genome’’ and DBI-1062301 "Barcoding-Free Multiplexing: Leveraging Combinatorial Pooling for High-Throughput Sequencing" to T.J.C. and S.L.; USDA-CSREES-NRI grant 2006-55606-16722 ‘‘Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement’’ to G.J.M., R.P.W., T.J.C.and S.L.;the Agriculture and FoodResearchInitiativePlantGenome,Genetics and Breeding Program of USDA-CSREES-NIFA grant 2009-65300-05645 ‘‘Advancing the Barley Genome’’ to T.J.C., S.L. and G.J.M.; BRAIN and NBRP-Japan grants to K.S., Japanese MAFF Grant (TRG1008) to T.M. A full list of acknowledgements is in the Supplementary Information.